Yes, there really are.
A fellow JET and I discovered two thrift stores in the Harajuku area of Tokyo: Chicago and Kinji. We had seen “hipster” Japanese youth sporting dress-pant capris, high tops and flannel shirts, but nothing could have prepared us for this. What would normally be considered the “best find” at any thrift store in the U.S. could be found here in the fashion district of Tokyo! Everything from Carhart overalls to kimonos, Kavu outdoor gear to business suits, and an endless supply of Birkenstock sandals and clogs could be purchased at these thrift stores. A pair of pants might cost you around 1950 yen (~ $25), a pair of Birkenstocks: 2950 yen, a great ugly sweater: 500 yen. I was in the market for a business suit. I found a hemp one, but I don’t think the Japanese would have considered it professional…and I looked like the female counterpart to Indiana Jones…so I went without.
Chicago Thrift Store actually has its headquarters in the U.S., and ships clothing around Tokyo, where it is marked up and sold as “highly fashionable” western wear. There’s a great New York Times article on the Tokyo Vintage Scene if you’re interested: http://www.nytimes.com/2008/08/18/style/18iht-FVINTAGE.1.15327985.html